[2023-06-17 11:44:21,125] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:44:21,127] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:44:21,127] [INFO] DQC Reference Directory: /var/lib/cwl/stg0591eef6-cafc-4238-a655-3b710a01a192/dqc_reference
[2023-06-17 11:44:22,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:44:22,563] [INFO] Task started: Prodigal
[2023-06-17 11:44:22,563] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb1dde4e-a0bb-4605-a984-9bf3b52b836a/GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna.gz | prodigal -d GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/cds.fna -a GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:44:25,441] [INFO] Task succeeded: Prodigal
[2023-06-17 11:44:25,441] [INFO] Task started: HMMsearch
[2023-06-17 11:44:25,441] [INFO] Running command: hmmsearch --tblout GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0591eef6-cafc-4238-a655-3b710a01a192/dqc_reference/reference_markers.hmm GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:44:25,699] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:44:25,701] [INFO] Found 6/6 markers.
[2023-06-17 11:44:25,725] [INFO] Query marker FASTA was written to GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/markers.fasta
[2023-06-17 11:44:25,726] [INFO] Task started: Blastn
[2023-06-17 11:44:25,726] [INFO] Running command: blastn -query GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/markers.fasta -db /var/lib/cwl/stg0591eef6-cafc-4238-a655-3b710a01a192/dqc_reference/reference_markers.fasta -out GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:26,438] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:26,442] [INFO] Selected 9 target genomes.
[2023-06-17 11:44:26,442] [INFO] Target genome list was writen to GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/target_genomes.txt
[2023-06-17 11:44:26,451] [INFO] Task started: fastANI
[2023-06-17 11:44:26,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb1dde4e-a0bb-4605-a984-9bf3b52b836a/GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna.gz --refList GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/target_genomes.txt --output GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:44:29,696] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:29,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0591eef6-cafc-4238-a655-3b710a01a192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:44:29,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0591eef6-cafc-4238-a655-3b710a01a192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:44:29,706] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:44:29,706] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:44:29,706] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	94.8834	245	259	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	94.8817	244	259	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	94.8686	245	259	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	94.853	246	259	95	below_threshold
Haemophilus pittmaniae	strain=NCTC13334	GCA_900186995.1	249188	249188	type	True	83.1952	159	259	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	81.5911	138	259	95	below_threshold
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	81.3696	156	259	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.2649	147	259	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	79.1109	135	259	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:44:29,708] [INFO] DFAST Taxonomy check result was written to GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/tc_result.tsv
[2023-06-17 11:44:29,708] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:44:29,708] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:44:29,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0591eef6-cafc-4238-a655-3b710a01a192/dqc_reference/checkm_data
[2023-06-17 11:44:29,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:44:29,733] [INFO] Task started: CheckM
[2023-06-17 11:44:29,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/checkm_input GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/checkm_result
[2023-06-17 11:44:47,030] [INFO] Task succeeded: CheckM
[2023-06-17 11:44:47,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:44:47,053] [INFO] ===== Completeness check finished =====
[2023-06-17 11:44:47,054] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:44:47,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/markers.fasta)
[2023-06-17 11:44:47,055] [INFO] Task started: Blastn
[2023-06-17 11:44:47,055] [INFO] Running command: blastn -query GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/markers.fasta -db /var/lib/cwl/stg0591eef6-cafc-4238-a655-3b710a01a192/dqc_reference/reference_markers_gtdb.fasta -out GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:47,957] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:47,964] [INFO] Selected 15 target genomes.
[2023-06-17 11:44:47,964] [INFO] Target genome list was writen to GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:44:47,976] [INFO] Task started: fastANI
[2023-06-17 11:44:47,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb1dde4e-a0bb-4605-a984-9bf3b52b836a/GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna.gz --refList GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/target_genomes_gtdb.txt --output GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:44:53,125] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:53,138] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:44:53,139] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003252755.1	s__Haemophilus_D parainfluenzae_N	95.8432	254	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.46	95.02	0.94	0.93	5	conclusive
GCF_000191405.1	s__Haemophilus_D parainfluenzae	94.853	246	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	-
GCF_001679485.1	s__Haemophilus_D sp001679485	94.4415	248	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	95.82	95.82	0.90	0.90	2	-
GCA_900756155.1	s__Haemophilus_D sp900756155	94.3746	242	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCF_014931275.1	s__Haemophilus_D sp900755445	94.3364	249	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCF_001815355.1	s__Haemophilus_D sp001815355	94.3194	244	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.35	95.20	0.94	0.91	8	-
GCF_003252795.1	s__Haemophilus_D parainfluenzae_K	94.2533	241	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
GCF_003252725.1	s__Haemophilus_D parainfluenzae_L	94.1231	238	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.33	95.18	0.90	0.88	7	-
GCF_014931395.1	s__Haemophilus_D sp900764435	94.0807	245	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.55	95.23	0.94	0.91	6	-
GCA_905207935.1	s__Haemophilus_D sp905207935	94.0235	214	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214375.1	s__Haemophilus_D sp905214375	94.0025	217	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
GCA_905215245.1	s__Haemophilus_D sp905215245	93.8249	223	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.18	95.12	0.97	0.97	5	-
GCF_003253005.1	s__Haemophilus_D parainfluenzae_M	93.7592	240	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
GCA_015255025.1	s__Haemophilus_D sp015255025	93.5124	214	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.38	95.17	0.91	0.91	3	-
GCA_900756875.1	s__Haemophilus_D sp900756875	93.5076	225	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.91	95.91	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-17 11:44:53,141] [INFO] GTDB search result was written to GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/result_gtdb.tsv
[2023-06-17 11:44:53,142] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:44:53,146] [INFO] DFAST_QC result json was written to GCA_905193665.1_ERR1190704-mag-bin.13_genomic.fna/dqc_result.json
[2023-06-17 11:44:53,146] [INFO] DFAST_QC completed!
[2023-06-17 11:44:53,146] [INFO] Total running time: 0h0m32s